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I-TASSER results for job id Rv2663

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

 Input Sequence in FASTA format
 Predicted Secondary Structure
 Predicted Solvent Accessibility
 Predicted Normalized B-facotr
 Top 10 threading templates used by I-TASSER
 Top 5 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5, 2], where a C-score of higher value signifies a model with a high confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated. This is usually an indication that the models have a good quality because of the converged simulations.)
 Proteins structureally close to the target in PDB (as identified by TM-align

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB that have the closest structural similarity, i.e. the highest TM-score, to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)


 Predicted function using COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results from the COFACTOR, TM-SITE and S-SITE programs.)


  Ligand binding sites

Rank C-score Cluster
size
PDB
Hit
Lig
Name
Download
Complex
Ligand Binding Site Residues
10.08 4 1ofzA FUL Rep, Mult 17,24,50,66,72
20.08 4 1lqkA MN Rep, Mult 10,51
30.06 3 4oa5C IOD Rep, Mult 12,13,16
40.04 2 3sz5A MG Rep, Mult 42,44,51
50.04 2 2zu0B III Rep, Mult 2,3,6,7,10,11,12,20,24
60.04 2 1py2B ZN Rep, Mult 19,23
70.02 1 1p6bA ZN Rep, Mult 10,44
80.02 1 1lu1A ADE Rep, Mult 40,41,42,51,53,63
90.02 1 2ih9B 5AX Rep, Mult 10,11
100.02 1 2qtkB C8E Rep, Mult 39,62,63
110.02 1 1jb0M CLA Rep, Mult 16,20
120.02 1 1ugiC IMD Rep, Mult 6,25
130.02 1 3srgA CA Rep, Mult 25,64
140.02 1 3b04D MG Rep, Mult 64,66

Download the all possible binding ligands and detailed prediction summary.
Download the templates clustering results.
(a)C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)Cluster size is the total number of templates in a cluster.
(c)Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column.
Mult is the complex structures with all potential binding ligands in the cluster.

  Enzyme Commission (EC) numbers and active sites

RankCscoreECPDB
Hit
TM-scoreRMSDaIDENaCovEC NumberActive Site Residues
10.0603b9jJ0.5083.370.0290.8831.17.1.4,1.17.3.27
20.0602vuaA0.3324.200.0300.6623.4.24.6921,23,26,49
30.0601httA0.4493.900.0900.8446.1.1.21NA
40.0603btaA0.4814.200.0810.9093.4.24.69NA
50.0602ebsB0.5273.470.0910.8313.2.1.150NA
60.0602gepA0.5093.770.0000.9221.8.1.2NA
70.0603c75J0.4863.530.0460.8051.4.99.3NA
80.0601zxiC0.5263.300.0570.8961.2.99.2NA
90.0601p4nA0.4804.150.0420.8832.3.2.10NA
100.0602zt5A0.4894.110.1000.8966.1.1.14NA
110.0601vp2A0.4833.880.1140.8833.6.1.157,55
120.0601cruB0.4993.680.0750.8441.1.5.2NA
130.0601c7kA0.4973.790.0900.8573.4.24.77NA
140.0603dslA0.5013.840.0290.9093.4.24.4934,39
150.0601jroB0.5013.290.0560.8961.1.1.204NA
160.0603epsA0.4963.840.0560.8832.7.11.530
170.0601ffuC0.5253.210.0850.8961.2.99.2NA
180.0602vxoB0.4963.760.1270.8576.3.5.2NA
190.0602aj4A0.4872.880.0420.7142.7.1.611,13

(a)CscoreEC is the confidence score for the EC number prediction. CscoreEC values range in between [0-1];
where a higher score indicates a more reliable EC number prediction.
(b)TM-score is a measure of global structural similarity between query and template protein.
(c)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d)IDENa is the percentage sequence identity in the structurally aligned region.
(e)Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided
by length of the query protein.

  Gene Ontology (GO) terms

Homologous GO templates in PDB 
RankCscoreGOTM-scoreRMSDaIDENaCovPDB HitAssociated GO Terms
00.070.5952.910.120.942gu1A GO:0046872
10.070.5413.360.090.883sluB GO:0016020 GO:0016021
20.070.5743.440.040.974rnyA GO:0016020 GO:0016021 GO:0046872
30.060.3634.870.100.864wl2A GO:0016787 GO:0016811
40.060.3414.810.030.771jmoA GO:0004866 GO:0004867 GO:0005576 GO:0005615 GO:0006935 GO:0007596 GO:0007599 GO:0008201 GO:0008218 GO:0010466 GO:0010951 GO:0030414 GO:0070062
50.060.4154.000.100.771o7dD GO:0003824 GO:0004553 GO:0004559 GO:0005764 GO:0005975 GO:0006013 GO:0006517 GO:0007611 GO:0008152 GO:0008270 GO:0015923 GO:0016787 GO:0016798 GO:0030246 GO:0046872
60.060.3853.760.040.703ihjA GO:0003824 GO:0004021 GO:0005739 GO:0005759 GO:0006103 GO:0008483 GO:0008652 GO:0009058 GO:0016740 GO:0030170 GO:0042851 GO:0042853
70.060.3974.260.060.731qwyA GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0009405 GO:0016787 GO:0046872 GO:0071555
80.060.2824.370.050.604lxcA GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0046872 GO:0071555
90.060.2744.130.040.514yorA GO:0004527 GO:0090305
100.060.3394.010.060.643tufB GO:0016020 GO:0016021 GO:0030435 GO:0042601
110.060.3853.960.040.693gm5A GO:0016829
120.060.3553.890.060.624bh5A GO:0000920 GO:0001896 GO:0005886 GO:0007049 GO:0009273 GO:0016787 GO:0030288 GO:0032153 GO:0042493 GO:0042597 GO:0051301 GO:0051345
130.060.4193.770.050.691phnB GO:0009507 GO:0009535 GO:0009536 GO:0009579 GO:0015979 GO:0016020 GO:0018298 GO:0030089 GO:0055114
140.060.3583.930.060.683ezjG GO:0006810 GO:0008565 GO:0009279 GO:0009306 GO:0015627 GO:0015628 GO:0019867
150.060.3563.820.050.653k57A GO:0000166 GO:0003676 GO:0003677 GO:0003887 GO:0006261 GO:0006281 GO:0006974 GO:0008296 GO:0008408 GO:0009432 GO:0016740 GO:0016779 GO:0045004 GO:0071897 GO:0090305
160.060.3353.540.030.603it5A GO:0004175 GO:0004222 GO:0005576 GO:0006508 GO:0008233 GO:0008237 GO:0009405 GO:0016787 GO:0046872
170.060.3323.900.050.615csnA GO:0001726 GO:0005102 GO:0005509 GO:0005576 GO:0005615 GO:0005634 GO:0005737 GO:0007409 GO:0007417 GO:0007611 GO:0007613 GO:0008270 GO:0008283 GO:0008284 GO:0008360 GO:0042802 GO:0042803 GO:0043025 GO:0043065 GO:0043123 GO:0043231 GO:0044548 GO:0045087 GO:0046872 GO:0048156 GO:0048168 GO:0048306 GO:0048471 GO:0048708 GO:0050786 GO:0050806 GO:0051384 GO:0051597 GO:0060291 GO:0071456 GO:2001015
180.060.2954.730.000.622hsiB GO:0046872


Consensus prediction of GO terms
 
Molecular Function GO:0046872 GO:0008201 GO:0004867 GO:0016811
GO-Score 0.13 0.07 0.07 0.07
Biological Processes GO:0006935 GO:0007596 GO:0010951 GO:0008218
GO-Score 0.07 0.07 0.07 0.07
Cellular Component GO:0016021 GO:0070062 GO:0005615
GO-Score 0.13 0.07 0.07

(a)CscoreGO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.
(b)TM-score is a measure of global structural similarity between query and template protein.
(c)RMSDa is the RMSD between residues that are structurally aligned by TM-align.
(d)IDENa is the percentage sequence identity in the structurally aligned region.
(e)Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.
(f)The second table shows a consensus GO terms amongst the top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on CscoreGO of the template.

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]



Please cite the following articles when you use the I-TASSER server:
1. J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2. J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.